Metagenome Normalization and Feature Selection

Published

22 Oct 2025

Load Libraries

Code
##################
# LOAD LIBRARIES #
##################
library(tidyverse)
library(mixOmics) 
library(readxl)
library(cowplot)
library(RColorBrewer)
library(scales)
select <- dplyr::select
map <- purrr::map

# setwd("/Users/vilkal/work/Brolidens_work/Projects/Candida-omics/src")

taxonomy <- c(
  "kingdom",
  "phylum",
  "class",
  "order",
  "family",
  "genus",
  "species",
  "strain"
)

The first part of this script follows the preprocessing steps outlined on the MixOmics tutorial https://mixomics.org/mixmc/mixmc-preprocessing/

data_path <- "/Users/vilkal/work/Brolidens_work/Projects/Candida-omics/Tidy_data/Metagenomics/Metageonome_all_vagswab_metaphlan.csv"
meta_path <- "/Users/vilkal/Downloads/Metadata_svamp.xlsx"

#############
# LOAD DATA #
#############
data <- read_csv(data_path) 
Rows: 682 Columns: 170
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr   (1): clade_name
dbl (169): zymomock_ex_1, neg_ex_1, neg_ex_2, zymomock_ex_2, neg_ex, zymomoc...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
meta_data <- read_xlsx(meta_path, sheet = "Metadata", skip = 1)
gr_data <- meta_data %>%
    rename(`Symptom score (0-5)` = "Symptom score (0-5) - ibland har de svarat olika skriftligt i frågeformuläret och muntligt vid inklusiion, då har jag valt den högsta scoren") %>%
  select(
    svamp_ID,
    `Fungal culture: C. albicans (y/n)`,
    `Fungal culture: Non-albicans candida spp. (y/n)`,
    `Symptom score (0-5)`,
    `Recurring fungal infections > 2/year (y/n)`
  ) %>%
    mutate(
  group = case_when(
    `Fungal culture: C. albicans (y/n)` == "1" &
      `Symptom score (0-5)` >= 1 &
      `Recurring fungal infections > 2/year (y/n)` == "1" ~
      "RVVCpos",

    `Fungal culture: C. albicans (y/n)` == "0" &
      `Recurring fungal infections > 2/year (y/n)` == "1" ~
      "RVVCneg",

    `Fungal culture: C. albicans (y/n)` == "1" &
      `Symptom score (0-5)` == 0 ~
      "AS",

    `Fungal culture: C. albicans (y/n)` == "0" &
      `Recurring fungal infections > 2/year (y/n)` == "0" ~
      "Control",

    `Fungal culture: C. albicans (y/n)` == "1" &
      `Recurring fungal infections > 2/year (y/n)` == "0" ~
      "Candidapos",

    TRUE ~ NA_character_
  )
) %>%
  select("svamp_ID", group, everything())

Step 2: Pre-filtering

keep taxa with at least 0.005% in at least 6% (2 out of 34) of samples, or at least 2% relative abundance in at least 1 sample.

# final
############################
# IDENTIFY TAXA TO FILTER #
###########################
t <- set_names(taxonomy, seq_along(taxonomy))
data <- data %>%
    select( -contains("ex"), -contains("seq"), -contains("_run2")) %>% # removes ctrl and extra samples
    select(-matches("_1W|_3M|_6M")) %>%
    mutate(
        level = factor(
            t[as.character(str_count(clade_name, "\\|") + 1)],
            levels = taxonomy),
            .after = "clade_name"
            ) 

n_samples <- select(data, starts_with("S")) %>% ncol() # number of good samples

# keep taxa with at least 0.005% in at least 6% (5 out of 84) of samples, or at least 2% relative abundance in at least 1 sample.

# Step 1. split clade name into seperate columns
temp <- data %>%
    separate(
    col = clade_name,
    into = taxonomy,
    sep = "\\|",
    #remove = FALSE,
    fill = "right"
  ) %>%
  # keeps any row where at least one numeric column has a value greater than zero
  filter(if_any(where(is.double), ~ .x > 0))

# Step 2. Identify the strains to remove
strains_to_remove <- temp %>%
  filter(level == "strain") %>%
  filter(
    !(rowSums(across(where(is.double), ~ .x > 0.005)) >=
      round(0.06 * n_samples) |
      rowSums(across(where(is.double), ~ .x >= 2)) >= 1)
  )

# pander table of strains to remove
strains_to_remove %>%
  arrange(desc(rowSums(across(where(is.numeric))))) %>%
  # removes samples with colsum = zero:
  select(
    -where(~ is.numeric(.x) && sum(.x) == 0)
  ) %>%
  knitr::kable(., digits = 1)
kingdom phylum class order family genus species strain level KX64 S02 S03 S04 S05 S09 S14 S17 S18 S20 S22 S23 S24 S25 S27 S29 S30 S31 S32 S35 S37 S38 S39 S43 S44 S46 S47 S49 S52 S53 S54 S55 S60 S61 S62 S64_BL S66_BL S67_BL S69_BL S70_BL S75_BL S76_BL S79_BL S81_BL S83_BL S84_BL S85_BL S86_BL S87_BL S89_BL S90_BL
k__Bacteria p__Actinobacteria c__Actinomycetia o__Bifidobacteriales f__Bifidobacteriaceae g__Bifidobacterium s__Bifidobacterium_bifidum t__SGB17256 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.7 0.0 0.0 0 0.0 0 0.0 0.0 0 0.1 0.0 0 0.9 1.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Peptostreptococcaceae g__Peptostreptococcus s__Peptostreptococcus_anaerobius t__SGB746 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.7 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 1.7 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Limosilactobacillus s__Limosilactobacillus_coleohominis t__SGB7100 strain 0.1 0.0 0.0 0 0.0 0 0.4 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.3 1.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_vaginalis t__SGB6696 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 1.3 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.3 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Eukaryota p__Ascomycota c__Saccharomycetes o__Saccharomycetales f__Debaryomycetaceae g__Candida s__Candida_parapsilosis t__EUK5480 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 1.1 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Mobiluncus s__Mobiluncus_curtisii t__SGB15487 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.1 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 1.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_sp_S7_1_8 t__SGB1501 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 1.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Limosilactobacillus s__Limosilactobacillus_vaginalis t__SGB7098 strain 0.0 0.7 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.2 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Atopobiaceae g__Lancefieldella s__Lancefieldella_rimae t__SGB985 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.9 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lacticaseibacillus s__Lacticaseibacillus_paracasei t__SGB7142 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.3 0.0 0.4 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_salivarius t__SGB8007_group strain 0.0 0.0 0.1 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.6 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Bacteroidales_unclassified g__Bacteroidales_unclassified s__Bacteroidales_bacterium_KA00251 t__SGB3324 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.6 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_vaginalis t__SGB29499 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.2 0 0 0.4 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_veroralis t__SGB1541 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.5 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Bifidobacteriales f__Bifidobacteriaceae g__Bifidobacterium s__Bifidobacterium_longum t__SGB17248 strain 0.0 0.0 0.0 0 0.2 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.3 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Enterobacterales f__Enterobacteriaceae g__Escherichia s__Escherichia_coli t__SGB10068 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.5 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.1 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Muribaculaceae g__GGB1460 s__GGB1460_SGB2023 t__SGB2023 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.2 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.1 0 0.0 0.0 0.0 0 0.0 0 0 0 0.2 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Winkia s__Winkia_neuii t__SGB17191 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.4 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Staphylococcaceae g__Staphylococcus s__Staphylococcus_hominis t__SGB7858 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.4 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Eggerthellales f__Eggerthellaceae g__Cryptobacterium s__Cryptobacterium_curtum t__SGB962 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.4 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Atopobiaceae g__Lancefieldella s__Lancefieldella_parvula t__SGB966 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.1 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Bifidobacteriales f__Bifidobacteriaceae g__Gardnerella s__Gardnerella_vaginalis t__SGB21500 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.3 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_corporis t__SGB1504 strain 0.0 0.0 0.0 0 0.0 0 0.1 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_buccalis t__SGB1514 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.2 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.1 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_melaninogenica t__SGB1547 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.3 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Arcanobacterium s__Arcanobacterium_sp_S3PF19 t__SGB17200 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.3 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__GGB1144 s__GGB1144_SGB1468 t__SGB1468 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.3 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pasteurellales f__Pasteurellaceae g__Haemophilus s__Haemophilus_haemolyticus t__SGB9649 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_duerdenii t__SGB6715 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Peptococcaceae g__Peptococcus s__Peptococcus_niger t__SGB4050 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_mitis t__SGB8185 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.1 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.1 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_bergensis t__SGB1505 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.1 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_gorbachii t__SGB6699 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.2 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_jeddahensis t__SGB6665 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_hydrogenalis t__SGB6663 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Veillonella s__Veillonella_atypica t__SGB6936 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.1 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_glucuronolyticum t__SGB17030 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.1
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_buccalis t__SGB1517_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinotignum s__Actinotignum_sanguinis t__SGB33732 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.1 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__Actinomyces_SGB17132 t__SGB17132_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Staphylococcaceae g__Staphylococcus s__Staphylococcus_epidermidis t__SGB7865 strain 0.0 0.1 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Eukaryota p__Ascomycota c__Saccharomycetes o__Saccharomycetales f__Debaryomycetaceae g__Candida s__Candida_dubliniensis t__EUK42374 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.1 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Eggerthellales f__Eggerthellaceae g__Slackia s__Slackia_exigua t__SGB14784 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Oscillospiraceae g__Mageeibacillus s__Mageeibacillus_indolicus t__SGB4002 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.1 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Mobiluncus s__Mobiluncus_mulieris t__SGB15486 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.1 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Schaalia s__Schaalia_turicensis t__SGB17195 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.1 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_unclassified g__Fenollaria s__Fenollaria_massiliensis t__SGB6716 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.1 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_amycolatum t__SGB17036 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.1 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_aurimucosum t__SGB17102 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.1 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Enterobacterales f__Enterobacteriaceae g__Salmonella s__Salmonella_enterica t__SGB10073 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_mitis t__SGB8168 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_tuscaniense t__SGB17076 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Lachnospiraceae g__Lachnospiraceae_unclassified s__Lachnospiraceae_bacterium t__SGB5267 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Lawsonellaceae g__Lawsonella s__Lawsonella_SGB3665 t__SGB3665 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_vespertina t__SGB1542 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_unclassified g__Eubacteriales_unclassified s__Clostridiales_bacterium_KA00274 t__SGB7884 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_pallens t__SGB1564 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Clostridiaceae g__Clostridium s__Clostridium_massiliamazoniense t__SGB29082 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__GGB10524 s__GGB10524_SGB17049 t__SGB17049 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Eggerthellales f__Eggerthellaceae g__Gordonibacter s__Gordonibacter_sp_Marseille_P4307 t__SGB14790 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_prevotii t__SGB6676 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Parvimonas s__Parvimonas_parva t__SGB6648 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Tenericutes c__Tenericutes_unclassified o__Mycoplasmoidales f__Metamycoplasmataceae g__Metamycoplasma s__Metamycoplasma_hominis t__SGB5926 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Listeriaceae g__Listeria s__Listeria_monocytogenes t__SGB7535 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Propionibacteriales f__Propionibacteriaceae g__Propionimicrobium s__Propionimicrobium_lymphophilum t__SGB15491 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_aurimucosum t__SGB17109 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_jejuni t__SGB1545 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Sutterellaceae g__GGB36599 s__GGB36599_SGB9269 t__SGB9269 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Varibaculum s__Varibaculum_cambriense t__SGB15482 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Finegoldia s__Finegoldia_magna t__SGB6686_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Atopobiaceae g__Atopobium s__Atopobium_minutum t__SGB987 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Urinicoccus s__Urinicoccus_massiliensis t__SGB29501 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_unclassified g__Levyella s__Levyella_massiliensis t__SGB5300 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pseudomonadales f__Pseudomonadaceae g__Pseudomonas s__Pseudomonas_aeruginosa t__SGB12320 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pasteurellales f__Pasteurellaceae g__Haemophilus s__Haemophilus_parainfluenzae t__SGB9712 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellia_unclassified f__Tissierellia_unclassified g__Ezakiella s__Ezakiella_coagulans t__SGB6728 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Lachnospiraceae g__GGB3883 s__GGB3883_SGB5265 t__SGB5265 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinotignum s__Actinotignum_timonense t__SGB17174 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pasteurellales f__Pasteurellaceae g__Mannheimia s__Mannheimia_massilioguelmaensis t__SGB9743 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_parasanguinis t__SGB8071 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Propionibacteriales f__Propionibacteriaceae g__Cutibacterium s__Cutibacterium_acnes t__SGB16955 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Neisseriales f__Neisseriaceae g__Neisseria s__Neisseria_subflava t__SGB9450_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Synergistetes c__Synergistia o__Synergistales f__Synergistaceae g__Jonquetella s__Jonquetella_anthropi t__SGB15495 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Porphyromonas s__Porphyromonas_uenonis t__SGB1974 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Micrococcales f__Brevibacteriaceae g__Brevibacterium s__Brevibacterium_sp_HMSC063G07 t__SGB23941 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Propionibacteriales f__Propionibacteriaceae g__Vaginimicrobium s__Vaginimicrobium_propionicum t__SGB33673 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinotignum s__Actinotignum_urinale t__SGB17176 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Megasphaera s__Megasphaera_micronuciformis t__SGB5868 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__Actinomyces_sp_ph3 t__SGB17137_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_oralis t__SGB8130 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_histicola t__SGB1543 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_gordonii t__SGB8053 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Bulleidia s__Bulleidia_extructa t__SGB6820 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__Actinomyces_sp_HMSC065F12 t__SGB17194 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Veillonella s__Veillonella_parvula t__SGB6939 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Veillonella s__Veillonella_dispar t__SGB6952 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Bacillales_unclassified g__Gemella s__Gemella_haemolysans t__SGB7285_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Dialister s__Dialister_pneumosintes t__SGB5842 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Senegalimassilia s__Senegalimassilia_anaerobia t__SGB14824_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Micrococcales f__Micrococcaceae g__Rothia s__Rothia_mucilaginosa t__SGB16971_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_uberis t__SGB110762 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__CFGB1705 o__OFGB1705 f__FGB1705 g__GGB4260 s__GGB4260_SGB5794 t__SGB5794 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Bifidobacteriales f__Bifidobacteriaceae g__Bifidobacteriaceae_unclassified s__Bifidobacteriaceae_bacterium_NR047 t__SGB33639 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_senegalensis t__SGB6664 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_nigrescens t__SGB1561 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_intermedius t__SGB8025 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Negativicutes o__Veillonellales f__Veillonellaceae g__Veillonella s__Veillonella_rogosae t__SGB6956 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__GGB1144 s__GGB1144_SGB1469 t__SGB1469 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_oris t__SGB1525 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Solobacterium s__Solobacterium_SGB6829 t__SGB6829 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Eukaryota p__Ascomycota c__Saccharomycetes o__Saccharomycetales f__Saccharomycetaceae g__Nakaseomyces s__Candida_glabrata t__EUK5478 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Carnobacteriaceae g__Granulicatella s__Granulicatella_SGB8239 t__SGB8239_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_simulans t__SGB17120 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_Family_XIII_Incertae_Sedis g__Mogibacterium s__Mogibacterium_diversum t__SGB3922_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Carnobacteriaceae g__Granulicatella s__Granulicatella_adiacens t__SGB8249 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Peptostreptococcaceae g__Peptostreptococcus s__Peptostreptococcus_sp_MV1 t__SGB747 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_australis t__SGB8059_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_constellatus t__SGB8026 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_grossensis t__SGB6701 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_sp_Marseille_P3915 t__SGB29506 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__Actinomyces_urogenitalis t__SGB15868 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Solobacterium s__Solobacterium_moorei t__SGB6826 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Mobiluncus s__Mobiluncus_SGB15488 t__SGB15488 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Epsilonproteobacteria o__Campylobacterales f__Campylobacteraceae g__Campylobacter s__Campylobacter_concisus t__SGB19351 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_urinimassiliensis t__SGB6736 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Atopobiaceae g__Lancefieldella s__Lancefieldella_parvula t__SGB964 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Schaalia s__Schaalia_SGB17158 t__SGB17158_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_murdochii t__SGB6671 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Micrococcales f__Micrococcaceae g__Rothia s__Rothia_mucilaginosa t__SGB16986 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_rachelemmaiella t__SGB109696 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinobaculum s__Actinobaculum_massiliense t__SGB17172 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_salivae t__SGB1522 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_baroniae t__SGB1533 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_prevotii t__SGB6679 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_sp_BV3C26 t__SGB6713 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Fusobacteriaceae g__Fusobacterium s__Fusobacterium_periodonticum t__SGB5989_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Fusobacteriaceae g__Fusobacterium s__Fusobacterium_gonidiaformans t__SGB5985 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Schaalia s__Schaalia_SGB17168 t__SGB17168 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Propionibacteriales f__Propionibacteriaceae g__Cutibacterium s__Cutibacterium_avidum t__SGB16953 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__Actinomyces_graevenitzii t__SGB17130_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Porphyromonas s__Porphyromonas_bobii t__SGB2043 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Olegusella s__Olegusella_massiliensis t__SGB960 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Corynebacteriales f__Corynebacteriaceae g__Corynebacterium s__Corynebacterium_atypicum t__SGB17094 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_harei t__SGB6693 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_nanceiensis t__SGB1536 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_Family_XIII_Incertae_Sedis g__Eubacteriales_Family_XIII_Incertae_Sedis_unclassified s__Eubacterium_sulci t__SGB3934_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pasteurellales f__Pasteurellaceae g__Haemophilus s__Haemophilus_pittmaniae t__SGB9656 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Carnobacteriaceae g__Granulicatella s__Granulicatella_SGB8255 t__SGB8255_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Bacillales_unclassified g__Gemella s__Gemella_haemolysans t__SGB7292 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_urinalis t__SGB8215 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Peptostreptococcaceae g__Peptostreptococcus s__Peptostreptococcus_SGB749 t__SGB749 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Varibaculum s__Varibaculum_cambriense t__SGB15481 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_sanguinis t__SGB8047_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotella s__Prevotella_sp_DNF00663 t__SGB3322 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Actinobacteria c__Actinomycetia o__Actinomycetales f__Actinomycetaceae g__Mobiluncus s__Mobiluncus_SGB15489 t__SGB15489 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_SGB6672 t__SGB6672 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Fusobacteriaceae g__Fusobacterium s__Fusobacterium_nucleatum t__SGB6001 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Bacteroidota c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Porphyromonas s__Porphyromonas_sp_HMSC065F10 t__SGB1990_group strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Clostridia o__Eubacteriales f__Eubacteriales_Family_XIII_Incertae_Sedis g__Eubacteriales_Family_XIII_Incertae_Sedis_unclassified s__Clostridiales_bacterium_S5_A14a t__SGB3977 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Fusobacteriaceae g__Fusobacterium s__Fusobacterium_nucleatum t__SGB6014 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Fusobacteriaceae g__Fusobacterium s__Fusobacterium_nucleatum t__SGB6011 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Streptococcaceae g__Streptococcus s__Streptococcus_infantis t__SGB8086 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Peptoniphilus s__Peptoniphilus_sp_Marseille_P3761 t__SGB29485 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
k__Bacteria p__Firmicutes c__Tissierellia o__Tissierellales f__Peptoniphilaceae g__Anaerococcus s__Anaerococcus_mediterraneensis t__SGB29507 strain 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0 0 0.0 0.0 0.0 0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0 0 0 0.0 0 0 0.0 0.0 0.0 0.0 0.0 0.0
# Step 3. Aggregate removed strains by higher levels
removed_all_lvls <- strains_to_remove %>%
  # pivot_longer(cols = where(is.double), names_to = "sample", values_to = "removed_abundance") %>%
  select(-level) %>%
  pivot_longer(
    cols = kingdom:strain,
    names_to = "level",
    values_to = "name"
  ) %>%
  nest(.by = c(level)) %>%
  mutate(
    data = purrr::map(
      data,
      ~ summarise(.x, across(where(is.double), ~ sum(.)), .by = c("name"))
    )
  ) %>%
  mutate(data = setNames(.[["data"]], .$level))

removed_all_lvls
# A tibble: 8 × 2
  level   data               
  <chr>   <named list>       
1 kingdom <tibble [2 × 94]>  
2 phylum  <tibble [8 × 94]>  
3 class   <tibble [16 × 94]> 
4 order   <tibble [26 × 94]> 
5 family  <tibble [43 × 94]> 
6 genus   <tibble [74 × 94]> 
7 species <tibble [154 × 94]>
8 strain  <tibble [164 × 94]>
knitr::kable(removed_all_lvls$data[[2]], digits = 1)
name KX63 KX64 S01 S02 S03 S04 S05 S06 S07 S08 S09 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 S29 S30 S31 S32 S33 S34 S35 S36 S37 S38 S39 S40 S41 S42 S43 S44 S45 S46 S47 S48 S49 S50 S51 S52 S53 S54 S55 S56 S57 S58 S59 S60 S61 S62 S63_BL S64_BL S65_BL S66_BL S67_BL S68_BL S69_BL S70_BL S71_BL S72_BL S73_BL S74_BL S75_BL S76_BL S77_BL S78_BL S79_BL S80_BL S81_BL S82_BL S83_BL S84_BL S85_BL S86_BL S87_BL S88_BL S89_BL S90_BL S91_BL
p__Firmicutes 0 0.1 0 0.8 0.1 0 0.0 0 0 0 0 0 0 0 0 0.4 0 0 0.0 0 0 2.0 0 0 0 0.1 0.8 0 0.4 0 0 0.0 0 0.0 0 0 0.0 0 0 0.0 0.3 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.1 0 0 0 0 0 0 0 0.0 0.0 0.1 0 0.0 0 0 0.0 0 0.2 0 0 0 0 0 0 0 0 0 0.2 0 0 0 0 3.2 0.3 0.2 0.4 0 0.4 1.0 0
p__Actinobacteria 0 0.0 0 0.0 0.0 0 0.2 0 0 0 0 0 0 0 0 0.0 0 0 0.1 0 0 0.4 0 0 0 1.3 0.0 0 0.0 0 0 0.0 0 0.1 0 0 0.1 0 0 0.1 1.3 0 0 0 0 0.9 0 2.2 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.2 0.0 0 0.2 0 0 0.4 0 0.0 0 0 0 0 0 0 0 0 0 0.1 0 0 0 0 0.7 0.0 0.0 0.0 0 0.0 0.1 0
p__Bacteroidota 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.1 0 0 0.0 0 0 0.3 0 0 0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 1.0 0 0 0.2 0.8 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.2 0.0 0.1 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 1.7 0.0 0.0 0.0 0 0.0 0.0 0
p__Tenericutes 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.0 0 0 0.0 0 0 0.0 0 0 0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0.0 0 0 0.0 0.0 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0
p__Proteobacteria 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.0 0 0 0.0 0 0 0.0 0 0 0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0.0 0 0 0.0 0.0 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.5 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 0.3 0.0 0.0 0.0 0 0.1 0.0 0
p__Ascomycota 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.0 0 0 0.0 0 0 0.0 0 0 0 0.0 0.0 0 0.0 0 0 1.1 0 0.0 0 0 0.0 0 0 0.0 0.0 0 0 0 0 0.0 0 0.0 0.1 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0
p__Synergistetes 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.0 0 0 0.0 0 0 0.0 0 0 0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0.0 0 0 0.0 0.0 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0
p__Fusobacteria 0 0.0 0 0.0 0.0 0 0.0 0 0 0 0 0 0 0 0 0.0 0 0 0.0 0 0 0.0 0 0 0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0.0 0 0 0.0 0.0 0 0 0 0 0.0 0 0.0 0.0 0 0 0 0 0.0 0 0 0 0 0 0 0 0.0 0.0 0.0 0 0.0 0 0 0.0 0 0.0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0 0.0 0.0 0.0 0.0 0 0.0 0.0 0
# Step 4. get longer format and add back clade_names
# function to get clade name
get_full_clade.fun <- function(df) {
  # This will add a new column called match_clade
  # with the full clade_name that ends with the string from tissue_renorm_filt$clade_name
  df %>%
    mutate(
      match_clade = map_chr(
        name,
        ~ {
          hit <- data$clade_name[str_detect(
            data$clade_name,
            paste0(.x, "$")
          )]
          if (length(hit) > 0) hit[1] else NA_character_
        }
      )
    ) %>%
    select(match_clade) %>%
    pull()
}

removals <- removed_all_lvls %>%
  unnest(cols = data) %>%
  mutate(clade_name = get_full_clade.fun(.))

#############################
# FILTER AT ALL TAXA LEVELS #
############################
# Step 5. Subtract from higher levels
data_filt <- data %>%
  # Join percentages to be subtracted
  left_join(
    select(removals, -name, -level),
    by = "clade_name",
    suffix = c("", "_rm")
  ) %>%
  # Subtract sample-wise values
  mutate(
    across(
      matches("^S\\d\\d$"),
      ~ .x - coalesce(get(paste0(cur_column(), "_rm")), 0)
    )
  ) %>%
  select(-ends_with("_rm"))

# --- Step 6: check and replace negatives ---
indx <- which(data_filt < 0, arr.ind = TRUE)
Warning in Ops.factor(left, right): '<' not meaningful for factors
if (nrow(indx) > 0) {
  neg_report <- tibble(
    neg    = map2_dbl(indx[,1], indx[,2], ~ data_filt[[.x, .y]]),
    remove = map2_dbl(indx[,1], indx[,2], ~ data[[.x, .y]]),  # original value from data
    col    = map_chr(indx[,2], ~ colnames(data)[.x]),         # column name
    tax    = map_chr(indx[,1], ~ data[[.x, 1]])               # taxon/clade name
  )
  
  message("Negative values found and replaced with 0:")
  print(neg_report)

  # --- Step 7: replace negatives with zero ---
  data_filt <- data_filt %>%
  mutate(across(where(is.numeric), ~ pmax(.x, 0)))
}
Negative values found and replaced with 0:
# A tibble: 2 × 4
         neg remove col   tax                                                   
       <dbl>  <dbl> <chr> <chr>                                                 
1 -0.0000100 0.0147 S54   k__Bacteria|p__Firmicutes|c__Tissierellia|o__Tissiere…
2 -0.0000100 0.145  S61   k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Cor…
# test
strains_to_remove %>% pull("S39") %>% sum(.)
[1] 2.42705
data_filt %>% filter(level == "genus") %>% pull("S39") %>% sum(.)
[1] 97.57293
#####################################
# RENORMALIZED FILTERED TAXA VALUES #
#####################################
# Step 6. Re-normalize so each sample sums to 100
data_filt_norm <- data_filt %>%
  group_by(level) %>%
  mutate(
    across(
      matches("^S\\d\\d$"),
      ~ .x * 100 / sum(.x, na.rm = TRUE)
    )
  ) %>%
  ungroup()

# test
data_filt_norm %>% filter(level == "genus") %>% pull("S39") %>% sum(.)
[1] 100

Save filtered table

data_filt_norm %>%
  #select(-Pos_Seq_Ctrl) %>%
  arrange(level) %>%
  write_csv(
    .,
    "../Results/MixOmic/Metageonome_all_vagswab_metaphlan_taxa_filt.csv"
  )
# data_filt_norm <- read_csv("../Results/Tissue_QC/Metageonome_all_vagswab_metaphlan_taxa_filt.csv")

Step 3: Centered Log Ratio (CLR) Transformation

For technical, biological and computational reasons, microbiome data is compositional such that they represent proportions or relative information. Proportional data are restricted to a space where the sum of all OTU proportions for a given sample sums to 1. Using standard statistical methods on such data may lead to spurious results. Likewise, any data that are compositional in nature are interpreted into relative counts. Hence, using a CLR transformation allows the circumvention of these spurious results.

There are two ways of log-ratio transforming the data in mixOmics:

Option 1: Some of our functions (pca, plsda) directly include the argument logratio = 'CLR', so all you need to do is include your filtered offset data and add this argument (see example below).
Option 2: Some functions currently do not include the logratio argument. In this case, you will need to use the logratio.transfo() function as shown below. You can also use this function if you only have access to TSS (proportions) data and those were not offset.

unlike 16S data which are returned as raw counts after pre-processing, shotgun metageome data is often already normalized into proportions. This is because direct counts aren’t very meaningful across different taxa/genomes. That is why we will go with option 2 for our data.

🔹 Shotgun metagenomics

  • You sequence all DNA in the sample, not just one marker gene.
  • Reads are mapped to reference genomes, genes, or functional categories.
  • Raw counts can be biased by factors like:
    • genome size
    • gene length
    • variable sequencing depth
  • Because of this, many sequencing facilities preprocess shotgun data to produce normalized relative abundances (proportions), so that samples can be compared more easily.

Typical outputs include:
- Relative abundance (%) of taxa
- RPKM / TPM / CPM for genes or functions

gr <- tibble(ID = colnames(data)[-c(1,2)]) %>% 
    left_join(., gr_data, by =c("ID"="svamp_ID")) %>%
    mutate(
      pos = case_when(
        `Fungal culture: C. albicans (y/n)` == "1" |
        `Fungal culture: Non-albicans candida spp. (y/n)` == 1 ~
        "pos",
        TRUE ~ "neg"
        ), .after="group")

Now we want to simplify the clade_name column so that:

  • For phylum / class / order / family / genus, only the relevant level is kept.
  • For species and strain, all levels are incuded down from genus,
    i.e. "Genus species" or "Genus species strain".
# string manipulation

# data_filt_norm <- read_csv("../Results/Tissue_QC/Metageonome_all_vagswab_metaphlan_taxa_filt.csv")

# Modify taxa labels 
data_filt_norm <- data_filt_norm %>%
  mutate(
    taxa = str_extract_all(clade_name, "(?<=k__|p__|c__|o__|f__|g__|s__|t__)[^|]+"),
    taxa = map2_chr(taxa, level, ~ {
      if (.y %in% c("species", "strain")) {
        # keep everything from genus onward
        start <- which(c("k","p","c","o","f","g","s","t") %in% substr(.y,1,1))
        paste(.x[start:length(.x)], collapse = " ")
      } else {
        # keep only the last element (current level)
        tail(.x, 1)
      }
    }),
    .after = "level"
  ) %>%
  select(-clade_name) %>%
  rename(clade_name = taxa)
# Create matrix for all levels of taxa
# NB! the majority(?) of mixOmics functions expect a format of
# samples as rows and features as columns, thus the transformation 
# is VERY important!
matrix <- data_filt_norm %>%
    #rename_with(~ str_replace(.x, "_BL$", ""), everything()) %>%
    nest(data = -level) %>%
    # filter(level == "strain") %>%
    mutate(
    data = map(
      data,
      ~ .x %>%
        column_to_rownames(var = "clade_name") %>%
        as.matrix() %>%
        t()
    )
  )

matrix
# A tibble: 8 × 2
  level   data            
  <fct>   <list>          
1 kingdom <dbl [93 × 2]>  
2 phylum  <dbl [93 × 10]> 
3 class   <dbl [93 × 20]> 
4 order   <dbl [93 × 31]> 
5 family  <dbl [93 × 56]> 
6 genus   <dbl [93 × 99]> 
7 species <dbl [93 × 220]>
8 strain  <dbl [93 × 244]>
# Specify levels you want to process
tax_levels <- c("order", "family", "genus", "species", "strain")


matrix <- matrix %>%
  # Apply CLR transformation and PCA to each level
  mutate(
    clr_data = map(data, ~ logratio.transfo(.x, logratio = "CLR", offset = 1))
  ) %>%
    mutate(across(2:3, ~set_names(.x, paste0(.data[["level"]]))))
write_csv(
  matrix,
  "../Results/MixOmic/Metageonome_vagswab_CLR_transformed.csv"
)
# matrix <- read_csv("../Results/MixOmic/Metageonome_vagswab_CLR_transformed.csv")
matrix <- matrix %>%
  # Filter matrix to only these levels
  filter(level %in% tax_levels) %>%
  
  # Apply CLR transformation and PCA to each level
  mutate(
    #clr_data = map(data, ~ logratio.transfo(.x, logratio = "CLR", offset = 1)),
    pca_res  = map(clr_data, ~ pca(.x)),
    plot = map2(pca_res, level, ~plotIndiv(.x, 
                group = gr$pos, ind.names = F, size.title = 9,
                title = paste0(.y))),
    plot2 = map2(pca_res, level, ~plotIndiv(.x, 
                group = gr$group, ind.names = F, size.title = 9,
                title = paste0(.y)))
  ) %>%
    mutate(across(2:5, ~set_names(.x, paste0(.data[["level"]]))))

# Plot PCA for selected levels
l <- get_legend(plotIndiv(matrix$pca_res[["genus"]], legend = T, group = gr$pos)$graph)

l2 <- get_legend(plotIndiv(matrix$pca_res[["genus"]], legend = T, group = gr$group)$graph)

p <- matrix$plot %>% map("graph")
p2 <- matrix$plot2 %>% map("graph")
plot_grid(
  plotlist = c(list(l),p),
  #labels = matrix$level,   # use taxonomy levels as labels
  ncol = 3
)

plot_grid(
  plotlist = c(list(l2),p2),
  #labels = matrix$level,   # use taxonomy levels as labels
  ncol = 3
)

There are no clear seperation between the labels at any of the taxa levels. A google search indicate that Some studies find family or genus level is often most informative. Im wondering weather I can combine the matrix for genus and species level and to the PLS-DA on that?

Now that the data is:

  • filtered for low abundant taxa
  • CLR transformed
  • offset added

Now we can move on to the Feature selection (PLS-DA) For this portion of the script we are following the MixOmics tutorial here: https://mixomics.org/mixmc/koren-bodysites-case-study/

Feature selection

We want to do use a Multivariate feature selection method (PLS-DA). Multivariate methods considers features collectively, accounting for their interplay and redundancy, aiming for “more accurate prediction”

# combined genus and species levels with neg and pos only
m <- cbind(matrix$clr_data$genus, matrix$clr_data$species)
g <- gr$pos

# genus only and withouth samples with NA values 
#m <- matrix$clr_data$genus[!is.na(gr$group),]
#g <- gr$group[!is.na(gr$group)]

basic.plsda = plsda(m, g, logratio = 'none', 
                          ncomp = 3)

# assess the performance of the sPLS-DA model using repeated CV
perf.plsda = perf(basic.plsda,  
                  validation = 'Mfold', 
                  folds = 5, nrepeat = 10, 
                  progressBar = FALSE)

# extract the optimal component number
optimal.ncomp <- perf.plsda$choice.ncomp["BER", "max.dist"] 

plot(perf.plsda, overlay = 'measure', sd=TRUE) # plot this tuning

Tuning of the model

grid.keepX = c(seq(5,150, 5))

tune.splsda = tune.splsda(m, gr$pos, 
                          ncomp = optimal.ncomp, # use optimal component number
                          logratio = 'none', # transform data to euclidean space
                          test.keepX = grid.keepX,
                          validation = c('Mfold'),
                          folds = 5, nrepeat = 10, # use repeated CV
                          dist = 'max.dist', # maximum distance as metric
                          progressBar = FALSE)

# extract the optimal component number and optimal feature count per component
optimal.keepX = tune.splsda$choice.keepX[1:2] 
optimal.ncomp = tune.splsda$choice.ncomp$ncomp 

plot(tune.splsda) # plot this tuning

For each component (coloured according to the legend), the optimal number of features to select is shown by the large diamonds. This is selected per component using a one-sided t-test. The y-axis depicts the average correlation between the predicted and actual components. This is cross-validated over folds folds and repeated nrepeat times.

optimised model

splsd.mod = splsda(m, gr$pos, logratio= "none", # form final sPLS-DA model
                ncomp = 2, 
                keepX = optimal.keepX)

plotIndiv(splsd.mod,
          comp = c(1,2),
          ind.names = FALSE,
          ellipse = TRUE, # include confidence ellipses
          legend = TRUE, size.title = 9,
          legend.title = "Candida",
          title = 'sPLS-DA Comps 1&2')

png("cim_plot.png", width = 2000, height = 2000, res = 300)
cim(splsd.mod,
    comp = c(1,2),
    margins = c(10, 5),
    row.sideColors = color.mixo(factor(gr$pos)), # row colors by bodysite
    legend = list(legend = levels(factor(gr$pos))),
    title = 'Clustered Image Map of Koren Bodysite data')
dev.off()
quartz_off_screen 
                2 
plotVar(splsd.mod,
        comp = c(1,2),
        cutoff = 0.7, rad.in = 0.7,
        title = 'Correlation Circle Plot Comps 1&2')

png("network_plot_.png", width = 6.7, height = 6.7, res = 300, units = "in")
network(splsd.mod,
        size.node = 0.05, cex.node.name = 0.5,
        cutoff = 0.1, block.var.names = F, plot.graph = FALSE,
        color.node = c("orange","lightblue"))

dev.off()
quartz_off_screen 
                3 

evaluate PLS-DA

# evaluate classification, using repeated CV and maximum distance as metric
perf.splsda = perf(splsd.mod, validation = 'Mfold', 
                         folds = 5, nrepeat = 10, 
                         progressBar = FALSE, dist = 'max.dist') 

perf.splsda$error.rate
$overall
       max.dist
comp1 0.3258065
comp2 0.2989247

$BER
       max.dist
comp1 0.3229417
comp2 0.2966004

Taxa selection

par( mfrow= c(1,2) )
p <- map(c(1,2), ~plotLoadings(splsd.mod, comp = .x, 
             method = 'mean', contrib = 'max',  
             size.name = 0.8, legend = FALSE, size.title = 1,
             ndisplay = 20, style = "ggplot2",
             title = paste0("Loadings of Component ",.x)) )
'ndisplay' value is larger than the number of selected variables! It has been reseted to 5 for block X

# determine which OTUs were selected
selected.OTU.comp1 = selectVar(splsd.mod, comp = 1)$name 
selected.OTU.comp2 = selectVar(splsd.mod, comp = 2)$name 

# display the stability values of these OTUs
perf.splsda$features$stable[[1]][selected.OTU.comp1] 

        Candida_albicans                Dialister Dialister_micraerophilus 
                    1.00                     0.96                     0.88 
             Megasphaera                   GGB754 
                    0.48                     0.30 
perf.splsda$features$stable[[2]][selected.OTU.comp2] 

                        Megasphaera                  Megasphaera_lornae 
                               0.94                                0.94 
                            GGB3012                     GGB3012_SGB4003 
                               0.94                                0.94 
                             GGB753    Limosilactobacillus_coleohominis 
                               0.94                                0.96 
                      GGB753_SGB989              Lactobacillus_jensenii 
                               0.94                                0.94 
                      GGB754_SGB990              Lancefieldella_parvula 
                               0.86                                0.92 
      Coriobacteriales_unclassified Coriobacteriales_bacterium_DNF00809 
                               0.88                                0.88 
           Streptococcus_agalactiae    Corynebacterium_glucuronolyticum 
                               0.92                                0.88 
                     Lancefieldella                              GGB754 
                               0.92                                0.82 
              Porphyromonas_uenonis                       Porphyromonas 
                               0.92                                0.90 
                     Staphylococcus                       Streptococcus 
                               0.88                                0.88 
      Limosilactobacillus_vaginalis            Anaerococcus_jeddahensis 
                               0.82                                0.86 
              Staphylococcus_aureus           Tissierellia_unclassified 
                               0.86                                0.82 
                    Corynebacterium        Lacticaseibacillus_paracasei 
                               0.86                                0.86 
                Prevotella_corporis                   Peptococcus_niger 
                               0.88                                0.88 
            Peptoniphilus_duerdenii            Haemophilus_haemolyticus 
                               0.88                                0.88 
     Tissierellia_bacterium_KA00581             Peptoniphilus_gorbachii 
                               0.84                                0.88 
                    GGB1144_SGB1468                         Gardnerella 
                               0.88                                0.82 
          Anaerococcus_hydrogenalis               Gardnerella_vaginalis 
                               0.80                                0.82 
                   Prevotella_amnii                             GGB1144 
                               0.78                                0.82 
                           Sneathia                         Haemophilus 
                               0.78                                0.82 
                Veillonella_atypica                Actinomyces_SGB17132 
                               0.78                                0.82 
                        Peptococcus                           Atopobium 
                               0.82                                0.80 
                Prevotella_buccalis                  Peptostreptococcus 
                               0.80                                0.94 
               Prevotella_veroralis                             Gemella 
                               0.88                                0.78 
  Corynebacterium_pyruviciproducens                  Sneathia_vaginalis 
                               0.80                                0.70 
                Schaalia_turicensis                Prevotella_bergensis 
                               0.78                                0.78 
               Prevotella_denticola                      Slackia_exigua 
                               0.86                                0.78 
                Streptococcus_mitis                 Peptoniphilus_coxii 
                               0.76                                0.80 
                   Escherichia_coli                         Actinomyces 
                               0.76                                0.72 
          Anaerococcus_lactolyticus                   GGB73389_SGB46635 
                               0.74                                0.70 
                         Finegoldia                            GGB73389 
                               0.72                                0.82 
      Peptostreptococcus_anaerobius                 Salmonella_enterica 
                               0.82                                0.76 
                           Schaalia                    Atopobium_deltae 
                               0.72                                0.74 
            Lactobacillus_crispatus                    Parvimonas_parva 
                               0.68                                0.76 
              Prevotella_vespertina                  Prevotella_pallens 
                               0.74                                0.72 
                            Slackia                 Peptoniphilus_harei 
                               0.72                                0.68 
              Anaerococcus_prevotii                         Escherichia 
                               0.72                                0.70 
                    GGB1460_SGB2023                   Prevotella_jejuni 
                               0.68                                0.68 
                             Winkia              Listeria_monocytogenes 
                               0.54                                0.66 
                   GGB36599_SGB9269               Lactobacillus_gasseri 
                               0.66                                0.58 
             Pseudomonas_aeruginosa              Varibaculum_cambriense 
                               0.66                                0.66 
                         Salmonella                   Atopobium_minutum 
                               0.64                                0.62 
             Anaerococcus_vaginalis                  Neisseria_subflava 
                               0.58                                0.64 
                         Parvimonas            Urinicoccus_massiliensis 
                               0.64                                0.58 
         Haemophilus_parainfluenzae                        Anaerococcus 
                               0.58                                0.54 
             Actinotignum_timonense                    Finegoldia_magna 
                               0.58                                0.64 
     Mannheimia_massilioguelmaensis         Streptococcus_parasanguinis 
                               0.58                                0.58 
                Lactobacillus_iners                             GGB1460 
                               0.50                                0.56 
            Gemella_asaccharolytica                            GGB36599 
                               0.62                                0.54 
                           Listeria                         Pseudomonas 
                               0.56                                0.56 
                        Varibaculum                         Urinicoccus 
                               0.54                                0.54 
                          Neisseria                        Actinotignum 
                               0.54                                0.56 
               Streptococcus_oralis                          Mannheimia 
                               0.50                                0.56 
        Megasphaera_micronuciformis                  Actinomyces_sp_ph3 
                               0.58                                0.58 
                      Lactobacillus                Prevotella_histicola 
                               0.68                                0.56 
              Levyella_massiliensis              Streptococcus_gordonii 
                               0.42                                0.56 
                 Bulleidia_extructa                 Rothia_mucilaginosa 
                               0.56                                0.50 
                Cutibacterium_acnes                 Veillonella_parvula 
                               0.46                                0.50 
                 Veillonella_dispar              Dialister_pneumosintes 
                               0.48                                0.44 
         Senegalimassilia_anaerobia                      Granulicatella 
                               0.44                                0.52 
                       Winkia_neuii                       Cutibacterium 
                               0.50                                0.56 
     Clostridium_massiliamazoniense            Alloscardovia_omnicolens 
                               0.40                                0.62 
                    GGB4260_SGB5794                            Levyella 
                               0.44                                0.48 
                          Bulleidia           Anaerococcus_senegalensis 
                               0.50                                0.44 
                      Solobacterium               Prevotella_nigrescens 
                               0.50                                0.44 
          Streptococcus_intermedius                              Rothia 
                               0.44                                0.52 
             Anaerococcus_tetradius                 Veillonella_rogosae 
                               0.50                                0.42 
                   Senegalimassilia              Bifidobacterium_longum 
                               0.50                                0.42 
                        Clostridium                     GGB1144_SGB1469 
                               0.52                                0.42 
                    Prevotella_oris                             GGB4260 
                               0.44                                0.50 
           Streptococcus_salivarius               Solobacterium_SGB6829 
                               0.44                                0.44 
             Granulicatella_SGB8239              Mogibacterium_diversum 
                               0.44                                0.44 
            Granulicatella_adiacens           Peptostreptococcus_sp_MV1 
                               0.44                                0.44 
                      Mogibacterium             Streptococcus_australis 
                               0.50                                0.44 
         Streptococcus_constellatus                       Fusobacterium 
                               0.44                                0.50